Old Friends and New Negotiations
by tenaciouserr
Summary: A familiar face is found as Atlantis learns the complications of being in the San Francisco Bay. Very light Sheppard/Weir. First chapter takes place in the SGC, after that it's all Atlantis.
1. Chapter 1

**A/N:** I'm honestly really proud of this fic, I think it's the best I've written in a while. I'm sure the idea is cliche, but this idea was so strong that I just had to write it out. The first chapter takes part mainly in the SGC, but after this Atlantis and everyone who inhabits it will dominate the story. Comments are appreciated, they let me know if I'm doing something right or wrong. :)

_A While Ago:_

"Rodney!" John yelled from his seat in the jumper, looking over his shoulder at the other man who was rewiring the systems.

"I know, I know," Rodney yelled back, "I'm almost done."

Behind him both Ronon and Teyla were crouched just inside the jumper, and in front of them was a forest filled with hundreds of creatures charging right towards them. Ronon fired off another blast, knocking one of the creatures back but it only fumbled slightly before it joined in the charge again. "They are getting closer," Teyla announced.

"I know!" Rodney yelled, "telling me that they're coming closer every five seconds is not helping!"

"Well when they get here we're not going to be able to yell at you anymore," John yelled back, "because we'll all be dead! We already lost two teams on the planet, and I do not want to die because of a bunch of wildebeest stampeding wannabes!"

"They aren't even close to wildebeests, they're more like-" Rodney began as he fumbled with some wires.

"Rodney!" Teyla, Ronon and John yelled in unison.

"...buffalo?" Rodney finished as the lights to the jumper went on. Immediately Teyla and Ronon moved forward to their seats as John closed the back door and shot the jumper straight up, hitting a few branches in the process. Rodney didn't move to his seat until they were well off the planet and into the space surrounding it, headed toward the spacegate.

"I didn't fix the jumper," Rodney said, his brows furrowed as he furiously hit away at his computer.

"Sure you did," John said, "we're flying and everything."

"No, I mean, my calculations weren't done, I only needed a few more seconds of course, but I wasn't done."

"Well, whatever you did worked," Ronon shrugged. Rodney didn't reply, instead he just kept hitting away at his computer and recalculating the scenario to figure out what had malfunctioned with the jumper.

_Now:_

A woman ran across the forest floor, stopping in front of a stream. Toes attached to dirty and calloused feet hit the side of the steam as she leaned over, her matted hair covering her face as her dirty hand reached out for water and scooped it up, bringing it to her mouth. She was completely nude, her body infested with bug bites that had become welts.

A shot rang out across the forest. Her head jerked up in surprise and she made a small grunting noise and immediately jumped back behind a nearby tree. The sound of barking followed the shot across the forest, the sound moved closer and closer to her. Her entire body tensed as her head cocked from one side to the other.

The woman dove back into a few bushes, crouching into a tight ball. She lightly parted the front leaves of the bush, watching the area in front of her as a man, a boy and a dog approached. The dog was sniffing the ground when suddenly his head jerked up and he headed straight for the bush she was in.

She pushed the dog away, but he came back, licking her as he started barking. "Dad?" The boy asked the taller man, looking at the bush as it moved back and forth and their dog kept barking.

"A squirrel, maybe," the father replied. He tensed as the dog was pushed back, a human hand clearly the thing that was pushing him.

"Dad," the son said again, having also seen the hand.

"Stay here," the man replied cautiously, stepping forward to the bush. "Hey, you there," he said roughly as his dog ran up to him and started to bark again. The bush remained absolutely still.

Cautiously the man stepped forward, spreading the branches of the bush. He was startled to see the naked woman, who looked up to him with equal surprise. "I'm sorry," he responded, but then he noticed the wild look in her eyes, how matted her hair was, and how dirty she was. "Are you okay?"

Her jaw moved, as if she was trying to speak but couldn't. "Do you need help?" The man asked, his voice softer as her eyes moved back and forth, as if scanning his face for answers.

"H-" she stuttered and stopped then tried again, "help," she dragged out the word, her tone not quite what it should have been. "Help me?" She asked, the words were mutated but understandable. The man nodded.

"We'll get you out of here," he said calmly as he turned to his son. "Go get my phone," His son stared at him, "now!"

The woman startled at the order and he turned back to her quickly, lowering himself to her level as he calmly 'shhhd' her as if she were a child. He reached a hand out cautiously to her, and for a moment she just stared at it. He nodded to her, and she reached out and put her hand in it. He pulled her up slowly, then shrugged his coat off and placed it over her. The dog barked at her and she winced, pulling away from the man.

"Quiet," the man ordered the dog, who obediently responded by not barking. "It's okay," he cooed to the woman, who jerked her head at every small sound in the forest. He wondered what had happened to the poor soul, and gently guided her out of the forest and to the hospital.

-------

"Are we sure it's her?" Daniel Jackson asked.

"If not it's her doppelganger," Jack O'Neill replied. Daniel raised an eyebrow towards him, "been watching a lot of sci-fi lately."

"We should send somebody," Daniel said.

"Already did, she's on her way here now but she's in rough shape according to her doctors. You worked with her the most, they want you to talk to her."

Daniel frowned, "What about-"

"We're not telling them yet," Jack said. Daniel's frown deepened, he opened his mouth to protest but Jack raised his hands and spoke over him, "We need to make sure. How would you feel in their position?"

"I'd want to know," Daniel replied, his brow furrowing in annoyance.

"If it turns out we're wrong?"

Daniel frowned, but didn't respond, "When does she get here?"

Jack checked his watch, "Oh, about... fifteen minutes ago. We put her in holding room five." Daniel shook his head lightly at the other man, and the two of them ventured down the hall and to the holding room.

Inside the room the woman was pacing back and forth. She'd been washed and her hair had been brushed out and was now held in a loose ponytail; it fell to her mid-back. For clothes she'd been changed from hospital scrubs to a standard green stargate outfit.

When Daniel entered she was startled and moved back to the wall farthest from him. "It's okay," he told her, "my name is Daniel Jackson. We know each other. Do you remember anything?"

She shook her head quickly. "Can you speak?" He asked, moving closer to her slowly so that she wasn't intimidated. She pulled back slightly, but not as much as before.

"Y-yes," she nodded, "haven't... had... to," her words were slow, but more understandable than they had been before. Daniel nodded, he gently reached out and held her by the elbow. She looked down but didn't flinch and he lightly guided her to one of the chairs positioned at the table in the middle of the room. He pulled two chairs out so that they were facing each other and placed her in one while he sat in the other.

"Do you know how long you were in the woods?"

She shook her head, "No... lost count."

"And you're sure you remember nothing?"

"I-" she paused, "I remember how to do things... I remember words and meaning... words from different languages too. At first... I didn't. I do now."

"That's good," he nodded.

"You're... Daniel?" She asked. He nodded, smiling gently at her. "You know me..." her voice trailed off.

"Yes," he supplied, "we've worked together before." He paused, lowering his eyes from her as he considered his options, "You see... we're not quite sure what's going on. You're suppose to be dead. Not that I'm one to judge coming back from the dead," he added wryly.

Her eyes studied his face for a moment, more focused than he'd seen them since he'd first walked in. "Who am I?"

"Dr. Elizabeth Weir," he said quietly. "You use to broker treaties for the UN, you were temporarily head of the SGC here, then you led the Atlantis expedition."

"Elizabeth," she repeated her name firmly. "I'm not dead," it wasn't a question, simply a statement.

"No," Daniel replied, "no, I guess you're not."

"Why?" She asked, then paused when she realized how open-ended the question was. "Why... should I be and why am I not?"

He paused, looking up the to the glass watching area where Jack and Landry were both watching. Jack nodded, the subtle cue was enough to let Daniel know that all the blood work they had double and triple checked had come back showing that she was, in fact, Elizabeth Weir.

"I really shouldn't be the one telling you this," Daniel replied, wishing once more that they had alerted Atlantis to the situation. After all, now that the city was cloaked in San Francisco they were just a phone call and plane trip away. But Jack had already been clear that they weren't to be told. He only knew the story from mission files he had read, but with a sigh he spoke again. "You led Atlantis," he began, going through the story to when she had downloaded into the replicator's body and eventually telling her how she had stepped through the Atlantis gate and into a spacegate.

She remained quiet as her eyes diverted to ground. "It's a lot to take in," Daniel offered.

"No, it makes sense... those words, I've known them all for a while," she said. Having been in the woods for so long and not in touch with the world or media she didn't find stargates or replicators incredible, simply words that she had slowly remembered. After another couple of moments she raised her head again, and for just a minute Daniel caught a glimpse of the woman who had negotiated with the goa'uld. "What happens now?"

"Well, that part we're not really sure about," Daniel admitted, "we want to keep you here for a while... just in case."

"Just in case?" She repeated, her eyebrows raising.

"Well, we've seen a lot here," Daniel admitted, "we want to make sure you are who we think you are."

She considered this for a moment, her mouth lowering into a frown, "I'm a threat." Daniel didn't respond, and for another moment they both simply sat in silence.

-------

"The IOA thinks she's a threat," General Landry mirrored her words at the meeting between himself, General O'Neill, Dr. Lam, and SG1 since they'd had the most contact with Elizabeth when she'd run the SGC.

"You can't really be talking about putting her in a cell for the rest of her life," Daniel practically yelled.

General Landry frowned, sitting at the front of the table with his hands clasped. Daniel continued, "She's a hero, she died for the Atlantis expedition... her negotiations with the goa'uld are part of the reason Ba'al and other system lords didn't attack us, she deserves the best we can give her."

"We have no idea if that woman is actually Dr. Weir!" Landry shot back.

"All her tests have come back positive," Dr. Lam said, "I couldn't say how but for all intensive purposes that woman is Elizabeth Weir, there's not even a trace of the replicator cells that were put into her body."

"Perhaps she is an alternate reality version of Elizabeth Weir," Teal'c suggested.

"Well," Samantha started as everyone's eyes inevitably turned to her, "I suppose that's possible... though there was no indication of any sort of technology that could have triggered that on her or in the forest she was found in. We've also never encountered amnesia with inter-dimensional travel."

"She's getting her memory back," Daniel insisted, "she said she didn't know words at first but now she can fully communicate. If we give her time she might be able to tell us how she got here herself."

"I'm with Jackson," Cameron said, "if the woman is the hero she's suppose to be we at least owe her the chance to speak for herself. We already have her under surveillance and she has a guard detail," he added, "so she poses no immediate threat." With Cameron's backing Daniel glanced imploringly towards Jack.

"Well, as much as I love to please the IOA," Jack began, "I say we give the woman a chance to prove herself one way or the other."

General Landry nodded, "my recommendation will be that we keep her here for observation. Though I doubt the IOA will appreciate that, they might want to hold a hearing on the matter."

Daniel nodded, "I'll go, speak on her behalf."

Landry nodded in agreement, "It's decided then."

The team shuffled to get up, and as they did so Vala smirked at Daniel, "Jealous?"

"What?" He asked, blinking at her.

"Well, if this Weir woman is who she says she is, you're not the only one who can die and come back," Vala grinned. Daniel rolled his eyes at her.

------

A month passed, and in that month the IOA managed to keep holding hearings on Elizabeth. Daniel presented her case again and again... and again. Eventually the IOA had conceded to let the SGC handle it as long as they were kept in the loop. Daniel was now comfortably in his office, going over recently found texts, when he heard a light knocking on the side of his open door.

"I am not jealous!" He groaned.

"That's good for you?" Elizabeth responded. He looked up in surprise.

"Oh, sorry... I thought you were Vala, somehow she managed to tag along to the hearing," he rubbed his hand over his face wearily.

"Ah, yes, Vala," Elizabeth smiled slightly, her speech back to what it had once been, "she's quite... interesting."

He smiled back at her, "How's your memory?"

"Getting to be almost recognizable," she smiled. "I remember most of my life... I think. I remember my dog and getting put in that limo and told about the stargate program," she shook her head, "I remember how crazy I thought the world had become when I found out. I remember Atlantis..." she paused. "I remember... living with the replicators..." her voice trailed off as she looked away from Daniel, pain etched across her face. "Then I came back... and then I was through the gate... that should have been it, I should have lost consciousness and been floating in space in that body permanently. I don't know why I'm here."

Daniel offered a small, sympathetic smile as Elizabeth turned back to look at him. "You'll remember," he offered.

She nodded, shaking off the doubt that was knotting in her stomach. "I wanted to thank you," she added, changing the subject, "for going up to bat for me."

"Yeah, well, I know how annoying it can be to die and come back... again," he offered.

"Still, I appreciate it," she said. "So, what are you working on?"

He motioned towards a small wooden stick that was sitting in the middle of his desk. "I'm trying to learn what this is, the writing engraved on it is from a few different languages, and once you wave your hand over it..." he did so, and a small flame lit at the top of it, but didn't burn the wood. "Sam can't figure out why it does that, so we think it's pretty advanced."

Elizabeth looked at the flame for a moment before quietly saying, "If you immediately know the candlelight is fire..."

Daniel's head jerked up, "Excuse me?"

"Oh, it's nothing, just one of those flashes of memory I have that doesn't make sense," she shrugged.

"What's the whole flash?"

"If you immediately know the candlelight is fire, then the meal was cooked a long time ago... I don't know what it's from, I thought maybe a riddle I'd heard sometime..." she stopped as Daniel just stared at her. "What?"

"I think we just figured out how you got back," he said quietly.


	2. Chapter 2

"Does the name Oma Desala ring a bell?" Daniel asked Elizabeth, now intently staring at her.

She bit her lip as she racked her memory, "Maybe, I don't know... it feels familiar."

"She's the ascended being that helped me to ascend when I was dying, that was one of a few little tidbits of information she told me to help me achieve the ascension. Evolutionarily speaking humans aren't exactly ready to ascend, but we can with a little help. We thought that Oma was in an eternal battle with Anubis."

"Wait..." Elizabeth grimaced as she lay her elbow on the table and her head collapsed into her hand.

"Elizabeth?"

"I- I'm seeing tidbits... things..." she let out a small grunt of pain. "I was in space... she... she spoke to me... my thoughts were hazy and disjointed so it took quite a while to understand." She rubbed her hand over her face, grimacing, "they... needed help. I helped them."

Her head jerked up as her eyes widened, "Rodney wasn't fast enough, they would have died."

"Atlantis," Daniel said, "you helped them?"

"No.." she frowned, the thoughts were become hazy and fragmented. "John... John's team... they were in a forest being charged... I helped them."

Daniel nodded in understanding, "Yeah, that kind of breaks the ascended rule book."

"I don't think it was the only time I did it. But how could I just watch?" She shook her head as the fragments of memories became hazy and unrecognizable. Then, with sudden clarity she looked at Daniel, "Oma wanted you to know she's fine. The ascended beings eventually stepped in and stopped Anubis... I think Morgan Le Fay had something to do with it..." she frowned, "I'm sorry, I don't remember anymore."

Daniel smiled sympathetically, "When Oma put me back after I broke the rules I couldn't remember what happened when I was ascended... at first I got small fragments of it but now I don't remember any of it."

"I ascended," Elizabeth said quietly. Then, with a sudden determination, "What does the SGC want to do with me? I haven't had guards in a few days, it means they believe me."

"The UN has agreed to take you back as a negotiator," Daniel offered.

"No," she stated bluntly, "is General Landry in his office?" Daniel nodded and she briskly exited his office and made her way through the SGC, leaving Daniel staring in surprise after her.

She stopped in front of Landry's door and knocked on it, "Enter."

"General Landry," she nodded politely to him as she entered and stood in front of him.

"Ah, Dr. Weir, the UN has agreed-"

"I know. I don't want the job."

"Excuse me?" Landry asked, clearly baffled by this response. "Do you have any idea how much work went into getting you that job back?"

"Yes, and I honestly appreciate it," Elizabeth responded calmly, "I appreciate how much effort everyone at the SGC has put in on my behalf. I want to go back to Atlantis."

General Landry stared at her as if she was losing her mind. "We still don't even know how you got here-"

"I ascended. Daniel helped me figure it out, I'm sure you'll be briefed later," she replied quickly.

Now he looked at her like she had lost her mind, "that may be, but even if that were so Richard Woolsey is the leader of the Atlantis expedition."

"I didn't say I wanted to lead Atlantis, I want to go back. Atlantis is my home, surely I'll be able to help the city in some capacity."

General Landry frowned, "I'm not sure-"

"I led the Atlantis expedition for three years," she insisted firmly, "I've more than proven my ability to negotiate and my worth as a member of the team. I'll start out as a janitor if I have to, for god's sake, but I am going back-" she raised her hands and turned away from Landry, fully intending to continue her rant. Instead she froze as her eyes looked at the doorway in front of her, "...to Atlantis," her voice was practically a whisper.

In front of her at the doorway stood John, and behind him were Rodney, Teyla and Ronon. "John," she said quietly, and after a brief pause she smiled widely and nodded to the rest of the team, "Rodney, Teyla, Ronon... it's good to see you."

Rodney was the one to break the awkward silence, "We left you in space," and then he turned to John as if to make it more official, "we left her in space."

"Perhaps it was not her," Teyla suggested. Ronon grunted lightly in agreement.

"Oh, no, that was me," Elizabeth replied, "I ascended."

Rodney's eyebrows rose in disbelief and surprise, "What? But I couldn't ascend!"

She smirked at him in amusement, "I had a little help."

John, who had watched the exchange in silence, looked to Landry who was clearly surprised by their arrival, "Woolsey found out. We've come pick her up. She belongs with us," he turned towards her, "if she is who she says she is."

"It's me," she said, and General Landry nodded a confirmation behind her. John said nothing, but simply nodded.

"Does Mr. Woolsey know you intend to take her back?"

"No, we're kidnapping her," Rodney rolled his eyes. General Landry only stared at him. "Okay, we might do that," he conceded, "but we're not."

General Landry sighed, "You can have her on a temporary trial basis, you must remain in contact and if anything goes wrong she will be returned to the SGC."

"Fine," John replied, "we can do that. Come on," he nodded to Elizabeth and then to his team as they headed back through the halls.

Teyla smiled at Elizabeth, "it is good to see you again," she offered.

Elizabeth smiled back, "how is your son?"

"Very well, thank you," Teyla replied.

"I've been teaching him," Rodney grinned, "you know, I figured he could use a genius to help raise his IQ early." Teyla rolled her eyes, but Rodney didn't even notice. Elizabeth smiled at the exchange.

"How did you get here so fast?" Elizabeth asked, the thought had occurred to her before but the sight of the team had been overwhelming.

"Oh, Atlantis is in San Francisco," Rodney shrugged.

"Atlantis... is in San Francisco?" Elizabeth repeated skeptically.

"Long story," Ronon replied, a small smirk forming on the side of his lips.

"Ronon died too," Rodney pointed out.

"Oh?" Elizabeth asked.

"Then he came back," Rodney nodded.

"Yep," Ronon said.

When they got up to the parking deck Elizabeth was surprised as they walked over to a very empty section of it. Realizing why they were there, she asked, "You brought the jumpers?"

"Eh, it was quicker," John replied, speaking for the first time since they'd left the office. "And Rodney needed practice."

"Rodney's driving? Across The United States?"

"Hey!" Rodney replied indignantly, "I can drive a puddle jumper... and we brought two."

"You brought two puddle jumpers?"

"One for Rodney, Teyla, and Ronon... one for me to save them if they crash," John replied.

"We raced," Rodney grinned. Elizabeth glared at him in disapproval. "I won," he added proudly.

"You cheated," John shot back, "you rigged yours to go faster."

"Well, yeah," Rodney shrugged, "why else would Ronon and Teyla have come with me?"

John shook his head lightly, both puddle jumpers were now revealed and side-by-side. "I'll get you on the way back," John said.

"Impossible," Rodney said, "want to beat him, Elizabeth?"

"Hm," she said, pretending to ponder the question, "I think I've died enough times, thank you."

That left her and John in one jumper, and Teyla, Ronon and Rodney in the other. She took the seat next to him as he started it, cloaked it again and shot it up into the sky. They both sat in silence until she finally spoke up, "John, listen, about what you said... when I was in FRAN's body, how I thought I was still Elizabeth but I wasn't."

He frowned, and opened his mouth to speak, but she shook her head and spoke before he had the chance, "No, you were right. More than you knew... I mean, it was me, but I was part replicator, my priorities were all wrong... all my morals were upside down..." she shook her head, letting out a small sigh.

"We heard everything you said in the office," John said slowly, then he looked over to her and for a moment their eyes met, "you're Elizabeth Weir... with longer hair." She smiled widely at him, the corners of her eyes glistening. "Now, let's kick Rodney's ass."

"Right," she let out a choked laugh as she shook off how touched she'd been by his acceptance of who she was. "Anything I can do to help?"

"Hold on," he replied, and just like that they shot forward and she was pushed back into her seat.

"How do we know where they are?" She asked, since both jumpers were invisible.

John motioned to the screen in front of her, "They're that dot, we're the one kicking their asses right here," he said as their dot passed Rodney's. Despite the childishness of the race, Elizabeth smiled as they passed Rodney.

"He's passing you," Elizabeth warned, her eyes intently on the screen.

"Yeah, he's got... rockets or something on the top of the jumper."

"Can you beat that?"

He grinned, "there's one thing Rodney doesn't understand, good piloting beats cool toys every time."

"You're still behind him," Elizabeth said, her eyes glued to the monitoring screen.

"Yup," John replied, a mischievous grin forming on his lips. They followed Rodney for a while before, suddenly, John shot out under him and moved in front of him. Elizabeth looked in front of her to see the San Fransisco Bridge.

"It's here?" She asked.

"Shielded," he nodded.

Rodney tried to shoot past him, but John shot down quicker and started to skim the water, announcing to Atlantis that they were entering. Despite Rodney's best attempts to catch up, they entered the docking bay first. "Yes!" Elizabeth called out triumphantly. John raised an eyebrow at her. She blushed slightly but smiled. "Good job."

He nodded, "welcome back. Ready to see the city?"

They docked the jumpers, and Rodney came out completely furious. "That was not possible," he insisted, "my jumper was faster!"

John shrugged innocently, "I guess it wasn't fast enough." Rodney frowned and crossed his arms, silently fuming as they walked into the city.

Elizabeth's eyes scanned everything, taking in the familiar sites of the city. "New view," John informed her as they entered the gateroom. She looked up to see the Golden Gate bridge. She looked back to the others before making her way up to the balcony, leaning over it as she sighed contently and looked at the city and then beyond to the bridge. John came up and leaned on the rail next to her, and she smiled at the nostalgia of the moment.

She sighed, knowing that she had to get to work making herself a spot here. "Where's Mr. Woolsey?"

"Not here," John replied, "it turns out putting an ancient city in the San Francisco Bay has a lot of paper work attached."

"You're in charge then?" She asked.

"Eh, yeah," he shrugged, "mostly I just have to yell at Rodney."

She stood, "where do you want me?" He looked at her in surprise, but didn't say anything. "You're in charge Colonel Sheppard," she said, all professionalism now, "I want to be of use to Atlantis, especially after..." her voice trailed off, she was unable to bring up the last time she'd been to Atlantis, how she had led the stray replicators to the city, the guilt it brought her, but he knew what she was talking about immediately.

He didn't speak for a moment, then he looked away from her, "We... still have some of your things... in boxes. You should take an empty room and unpack, change. Then I'll put you somewhere."

"Elizabeth?" She turned in surprise at the voice, Carson Beckett stood in front of her.

"Carson?" She exclaimed as he walked over to her and gave her a brief hug that she returned in surprise and happiness.

Rodney came up behind him, "I told you we should have told her first! This is actually our own little clone Carson."

"Aye, long story," Carson said. "It's good to see you."

She smirked, "I hear there have been a lot of those since I left. I'm glad to see you too."

"Rodney," John said, "take her to the nearest available room... and get her things."

Rodney nodded in understanding. She was touched that they had kept her personal belongings, and that they all seemed to know exactly where they were. Rodney led her to a warehouse-like room, where four boxes of her belongings were. He shoved two into her arms and then carried two himself. "So," he said as they began to walk towards her new room, "Jennifer, Dr. Keller and I, are dating."

"Oh, really?" Elizabeth asked, a little more surprise slipping into the question than she had intended. "That's great, congratulations."

"We only had to almost get frozen to death to figure it out," Rodney grinned, waving his hand over a sensor as they entered her new room. It was much smaller than her original room had been, but she was grateful to have it. Grateful that the team was at least accepting she was who she said she was, the strain of her last visit was clear but time would allow them to be where they had been, she hoped.

She put her two boxes on the bed, and Rodney put his on the floor. "It was actually pretty romantic, it turns out I can be romantic," he grinned widely. "Not that I ever had any doubts, I mean love is just a soft science..." Elizabeth wasn't listening anymore, she was looking around the room, her eyes distant in thought. "Right," he nodded, "I'll just let you settle in."

"Thank you, Rodney," she smiled at him.

He nodded, and turned to leave. Then he paused and turned back towards her, "I'm- we're really glad that you're back."

Her smile widened, "Thank you, I'm glad to be back." He nodded and then turned and left her on her own. She opened up the boxes one by one. The first three mostly consisted of clothes, it was the fourth box that made her pause. Inside was more clothes, on top of them were a few room decorations, but on top of the decorations was a picture of her dog and her father's pocket watch. What really surprised her was that while other things in the boxes had accumulated some dust, neither the picture nor the watch had. She was sure that someone had been cleaning them on a regular basis.

Her fingers ran over the face of the watch thoughtfully, then she quickly put the picture of her dog and the watch on the dresser next to her new bed and put her clothes away into the closet. She picked out an old outfit then changed from her SGC outfit and went back to find John.

He was in the control room, leaning on a computer panel. She paused as she heard Woolsey over the computer, "I'll be in Washington for at least another week it would seem. The US military not to mention quite a few other countries want a tour of the city."

"Are we giving them one?" John asked.

"We're not sure. China wants in on the tour and of course the US is secretly yet vehemently against that, and Russia is insisting that they receive full access to our technology, not to mention more than one scientist wants to study Ronon and Teyla."

"We're not going to let them though, right?" John was frowning now as he leaned forward on the panel.

"I honestly couldn't say," Woolsey said, though he didn't seem pleased with the idea either. "I'd personally rather go back to the Wraith than this," he groaned. Elizabeth smiled lightly, glad to see that command had agreed with the man's sense of humor and his character. "Is Elizabeth there?"

John turned to her, and she was surprised because she hadn't even known that he'd noticed her. "I'm here," she called, moving to stand beside him. "Thank you," she added, "for allowing me into Atlantis."

"It wasn't my idea," Woolsey replied. She turned to John who wouldn't meet her questioning glance. "I am glad to have you, though. Have you situated yourself?"

"Yes," she replied.

"Good, I'm sorry to say I just found out about you, we haven't really had time to find a place for you, for now if you'd like you can just help Colonel Sheppard however he sees fit."

"Of course," she replied.

"Alright," Woolsey sighed, "I have more meetings to be in. I'll call back in a day. Woolsey out."

She looked to John, her hands behind her back, "Where do you need me?" He frowned at the question, and began to shake his head.

"Please," she emphasized.

He pursed his lips and considered her for a second, "you speak a few languages, don't you? Rodney managed to connect to a few wavelengths from different countries... we're picking up chatter about Atlantis that might help Woolsey. You want to see if you can translate any of it?"

She didn't quite approve of this, but didn't question John's judgment. "Sure. I'll go to his lab right now." John nodded, a hardly noticeable smile on his face.

It was a start.

**A/N:** Comments are still appreciated. :) I hope this feels right to everyone else, I felt that Elizabeth going back to Atlantis would be a bit awkward and tense after everything that happened, so it's not all hugs and cuddles no matter how much I just want to write that.


	3. Chapter 3

**A/N:** I should probably have mentioned this is going to be in four parts, so just one part left after this. It's also fairly likely I'll include an epilogue, because I'm having quite a lot of fun writing this particular story. :) As always, comments are appreciated.

Elizabeth spent a few tedious days slumped over in front of a computer in Rodney's lab wearing a headset and transcribing the chatter Rodney had managed to connect to. "Anything?" Rodney asked her.

"Well, one of the Russian Dumas is a fan of pizza, as it turns out. Not just any pizza, pizza with anchovies," she sighed.

"Oh those are really good," Rodney replied. She made a half-attempt to a glare at him. "Well, keep at it," he offered her an awkward pat on her arm.

"Wait," she suddenly shot up from her slumped position."Rodney, come here, separate the recording for this part and about a minute back into it."

Rodney nodded as he hit away at the computer, "What is it?"

"I don't believe this," she said quietly, listening to the conversation intently. "Rodney, this is huge."

"Did he decide he prefers thick crust to thin?"

She shook off the joke, putting down the headset, "Russia is considering offering us a fully functional ZPM in exchange for some of their people permanently residing in the city."

"What?" Rodney asked skeptically, "How did they even get a full ZPM?"

"From what I could gather they found it with their stargate, sort a spare part. They don't actually have much use for it right now, so they've been saving it as a bargaining chip."

"That is huge," Rodney said, waving his hands as he spoke, "even when we got here the ZPM wasn't fully functional... with a fully functional one we could open parts of the city we've never even been in... we could do all that and still have enough energy to fly the city back out of here and to the Pegasus galaxy."

They both looked at each other for a moment before they practically dashed out of his lab and to the control room. "We found something," Rodney huffed when they both skidded to a halt in front of John.

"Well, she found something," Rodney amended, "I understood the technological possibilities of it," he grinned widely.

"Are you going to tell me what it is?" John asked, raising an eyebrow towards both of them.

"A ZPM!" Rodney stated triumphantly.

Elizabeth nodded, filling in the rest, "Russia wants to offer us one in exchange for access." John looked at them both for a moment, but suddenly a man behind him announced that a communication was coming in.

He turned and frowned, "Woolsey wasn't suppose to check in for another day, who is it?"

"Sir, the coded message appears to be in goa'uld."

"What?" Rodney exclaimed as John's frown deepened, "the goa'uld are mostly dead... SG1 killed them... it's how we found out about Atlantis in the first place."

"Patch it through," John said as he stood in front of the video screen. On the other screen the image of a blonde woman appeared.

"Atlantis," she said, her voice clearly goa'uld, "my name is Athena. I had heard the fabled city had landed on Earth but I had not thought it would be so easy to find. Are you the leader of the pathetic humans claiming to run the city?"

"Not exactly how I would have phrased it," John replied wryly, "what can we do for you?"

"You can give up the city to my control," Athena replied.

"I'm going to go with... no." John said.

"If you do not give up the city I will alert all media outlets to your existence and location. It would be unwise to decline my offer. I will contact you again in an hour, I would suggest by then you prepare to leave the city." The transmission cut off, leaving the room in silence.

"Contact Woolsey," John ordered, "connect him to the conference room. Inform the SGC too, see if we can find her in an hour." The man nodded affirmatively.

"Elizabeth, with me," he said as he started to walk, "Rodney, prepare all the city's defenses... see if we can move the city at all."

Rodney frowned, "We haven't got the power-"

"Just do it," John ordered, and Rodney continued to frown but remained silent and made his way back to his lab. John continued to walk until he reached the conference room, once inside he turned to her and she noticed the slight slump in his shoulders. "Thoughts?"

"She's bluffing," Elizabeth replied immediately. "If she contacted the city she probably knows where it is, but if she truly wants it for herself she wouldn't dare deal with the insanity that would come in revealing it."

John nodded slowly, "What the hell does a goa'uld want with a whole city, anyway?"

"Power," Elizabeth replied firmly, "the goa'uld have lost it. I've never heard of this goa'uld so it's likely she's a small player in the game. If she manages to get Atlantis the goa'uld will have a chance to rise up again, with her as their leader."

"Sir, Mr. Woolsey is connecting in now," a voice informed them. John nodded and took a seat, Elizabeth followed his lead and took the seat next to his.

"Colonel Sheppard?" Woolsey asked, his voice emitting across the room.

"Yeah," John replied, "we may have a minor problem."

"How minor?"

"A goa'uld called Athena is threatening to reveal Atlantis if we don't give it to her. She's given us an hour ultimatum."

There was a pause, and John spoke again, "but we think Russia is going to offer us a ZPM," he offered it with a false sense of cheeriness.

"I can't possibly be there in an hour," Woolsey said, "who else is there?"

"It's me and Elizabeth. I've already sent Rodney to see what he can do about this." There was a very long pause, and for a minute Elizabeth thought the connection had been lost.

"Dr. Weir," Woolsey said, "I'm giving you permission to speak on behalf of Atlantis and myself, as well as make any decisions that may arise. How imminent is this threat?"

"She's bluffing," Elizabeth reiterated. "I can stall her as long as you need me to."

"Good, I expect frequent updates on the situation. Now, what about Russia and a ZPM?"

"We've been tracking their conversations," John replied, "Russia is considering offering a ZPM for access to the city."

"Well let's hope they do," Woolsey said quietly, "keep me informed. Woolsey out."

"Got a plan?" John asked her.

"I was thinking of not letting them have the city," she replied wryly.

"Good plan," he nodded, a small smile forming on his lips. She smiled back. "I'll have someone get you a file on Athena. Anything else you'll need?"

"No, thank you," she replied. He nodded, quickly leaving her on her own in the room. She let out a small sigh, she'd just returned from the dead and now she was about to talk to a goa'uld... again. She knew this was her chance to prove herself but she couldn't help but feel ill-prepared for the situation. She stood, letting out a final sigh, it wasn't like that ever mattered.

Exactly an hour from her last transmission, Athena called in again. Elizabeth stood in front of the screen, her chin raised and her hands clasped behind her back. "Where is the little man who leads Atlantis?" Athena demanded.

"I am Dr. Elizabeth Weir," she said, "I speak on behalf of Atlantis."

"Have you made your decision?"

"We have considered your offer," Elizabeth nodded, "at this time we're not willing to give up the city."

"I will tell the media," Athena hissed.

"What will you tell them?" Elizabeth asked calmly, "That an ancient city has been found? Seeing is believing and we cannot be seen. Footage of an empty area doesn't really sell like it used to." She was careful to not give away the location of the city, just in case.

"Ma'am," she turned in surprise to the man operating the computer next to her, "we have a new message... it's in Russian."

She frowned before turning back to Athena, who was clearly annoyed. "I don't know who you think you are," the goa'uld hissed.

"You know," Elizabeth said, cutting her off, "I'm sure the tok'ra would love to know that there's a goa'uld running around. Why don't you come to the city yourself and we'll cut you out of that body you're so cozy in?"

Athena let out a growl, "I will call back in a day, if you still remain so... insubordinate I will take action." The transmission cut off.

"Why are Russians contacting us?" Elizabeth demanded, turning back to the man who had spoken.

"They're... calling in..." the man replied, "would you like them on screen?" Elizabeth frowned, looking up to John who had watched the whole exchange. He nodded and she confirmed, "Put them up."

"Greetings, Atlantis," the man on the screen said, a heavy accent clear in his voice.

"How were you able to contact us?" Elizabeth asked.

"Richard Woolsey has told me to contact you," the man said, "he wished to allow us first access to the city."

At first all she felt was relief, Woolsey had recovered the ZPM and was letting Russia in on Atlantis. Then, another thought occurred to her. Her eyes narrowed at the man on the screen as she crossed her arms. "Mr. Woolsey has not informed us of this."

"Perhaps communications are running slow?" The man suggested. Her eyes narrowed even more at him.

"Why did Mr. Woolsey agree to that?"

The man shrugged, "He believed we had the right to see it first."

She remained absolutely expressionless as she said, "How about you tell me what really happened?"

The man frowned heavily, "I have told you what happened."

"You've told me a lovely story," Elizabeth replied, "now I'm asking you to tell me how you were able to get in contact with us." She raised an eyebrow to the other man, who stared her down for a good minute before speaking.

"We were informed of your location and how to get in touch with you," he admitted.

"Who told you?"

"A blonde woman," the man shrugged. Elizabeth's mouth etched into a heavy frown.

She turned to the man sitting at the desk behind her, "send him a picture of Athena." The man nodded and hit away at a few buttons. "Is that the woman who told you?"

"Yes," the Russian man nodded.

"That woman is a goa'uld," Elizabeth practically hissed, "you were consorting with a goa'uld."

The man's eyes widened, he yelled back to the people behind him in Russian, Elizabeth followed the conversation of blame and surprise and then the man turned back to her, "We did not know that."

"Regardless," she spoke with a level of coldness now, "you just tried to enter our city against our wishes. Let me guess, the woman wanted to tag along with some of her people too?"

"Our promise of that was how we got the information," the man confirmed, "we did not know."

"You tried to break into our city," Elizabeth replied harshly, "and if you had succeeded you would have brought a goa'uld attack with you. That is not a good first impression."

"Surely we can amend this situation," the Russian man insisted. "Russia was hardly allowed into the Atlantis program, that must be changed."

"Forcing your way into the city is a mistake," Elizabeth said, "our terms now are simple: you give us your fully functional ZPM and we'll allow for one team of your choosing to join the expedition. One team only."

The man was fuming now, "You have been listening to us!"

"No doubt the goa'uld who sent you to us has too," Elizabeth said, aware that Russia had been chosen for a reason, Athena must have known about the ZPM and assumed Atlantis knew too, that or she had someone inside Atlantis already. Elizabeth shook off the thought, "Considering everything that's happened I fail to see us as being at fault here."

The man growled, and she heard him yell back in Russian to the men behind him. She wondered how high up the men were, it was very possible that the president himself was in the room, but she doubted whether she'd ever know for sure.

The man turned back to her, "What would our team be doing?"

"They would be like any other team here," she responded.

"We request a personal representative be sent there who can report back to us and represent our government in all decisions made," the man said.

"That's not how we work here," Elizabeth responded, "we will allow you to have a team here, if you'd like the team can report back to you, but we have only one leader. The other nations here have not been shown that kind of power, nor will you be."

"We wish to speak someone else," the man replied gruffly.

She felt John by her side in a second, "It won't do much good," he said, "the lady's in charge." She wanted to say something to that, but knew she couldn't break eye contact with the other man.

"How many people will be allowed on the team?" He practically huffed.

"Usually, four. I'm willing to allow you up to six," she replied.

"We will take no less than ten," the man said.

"Seven," Elizabeth replied quickly, having expected the argument.

"Eight," the man said, "absolutely no less."

"Fine," Elizabeth replied. "We'll pick up your team and allow them in on the condition that they bring the ZPM."

"Very well," the man replied, "we will have them prepared in a day." The transmission cut off and Elizabeth lowered her head and let out a sigh.

"Think Athena will call back?" John asked at her side.

"Probably... once she finds out we diverted her plan she won't be happy."

"Darn," John said. Elizabeth smiled at him.

"Okay," Rodney practically yelled as he came up to both of them, "there is no way I can get this city moved even an inch, it's absolutely impossible. I may be a genius but I am not a miracle worker-"

"Rodney-" John tried to interject.

"I mean really, there's only so much I can do. Granted, I can do quite a lot," Rodney smirked at this, "more than anyone else, really, but-"

"Rodney-" Elizabeth began.

"I can't move an entire city with no power! That's like... telling me to start a car without a motor!"

"Rodney!" John and Elizabeth yelled out in unison. He stopped in surprise.

"We got the ZPM," Elizabeth informed him.

His face lit up, "Really? How?"

"You can play with it when it gets here," John said with a slight smirk. "Him and his new toys," he said as he turned to Elizabeth.

"Sir, Mr. Woolsey is sending in a transmission."

"We're getting popular," John said sarcastically, nodding towards the screen.

"I see Atlantis is still intact. What's been happening?" Woolsey asked.

"Well," John said, "the goa'uld looks to be mostly full of hot air and we've got a ZPM coming our way in a day."

"How?" Woolsey asked, clearly surprised. John nodded towards Elizabeth, and she spoke up.

"I agreed to let a small team of Russians join Atlantis, they were unhappy with the ratio on the mission. Eight in total."

Woolsey frowned, "I don't know how I'll explain that to the other nations... still, eight for a ZPM? How did you convince them to that?"

"They tried to break in," Elizabeth said. Woolsey seemed alarmed at this news, "They lied to us and said you had allowed them passage in. It was a half-formed plan at best."

"Very well then... I'll be back there in a day's time."

"Don't you have meetings?" John asked.

"We have a ZPM," Woolsey said, "we're heading back to Pegasus. It's where the city belongs."

"Will the IOA be pleased with that decision?" Elizabeth asked, surprised by his response.

"They'll just have to live with it," Woolsey shrugged, "I've already discussed it with General Landry, in the possibility we did get the ZPM. He agreed our mission was best served there. Woolsey out."

"Did he-" Elizabeth began.

"Get a lot cooler when he came here?" John finished her sentence.

"I was going to go with 'stronger' but yes," she nodded.

"Yep."

"Oh," Rodney whined, "it's almost dinner time."

"Rodney McKay, I have never heard you so disappointed to find out it was dinner time," Elizabeth said, genuinely surprised.

"Ah, Teyla has been trying out some Earth cooking," John informed her.

"Oh, what does she cook?" Elizabeth asked.

"Well, we're not quite sure..." John admitted.

"Torren's the lucky one," Rodney whined, "he gets to keep on eating his own food. While we're all subject to her cooking."

John leaned over to Elizabeth, and in a fake whisper said, "I'm pretty sure Rodney's been stealing some of the kid's food."

"I wish," Rodney groaned. He sighed, "Ready for dinner?"

"He still eats the food?" Elizabeth asked John in surprise as the three of them began to walk forward.

"Keller makes him," he grinned at her.

"Hey!" Rodney yelled, "I make my own decisions." He puffed his chest out a little as if to prove how manly he was, it took all of Elizabeth's efforts not to burst out laughing. Instead she and John exchanged smirks behind his back.

They entered a room that had been set up with a table and chairs, a few steaming plates of food were set out in the middle of it. Teyla was gently nudging a dish to the middle of the table, while Dr. Keller and Ronon were already sitting at the table, a seat apart. Teyla raised her head and smiled widely, "I have cooked barbecue for tonight."

Elizabeth heard Rodney let out a long sigh before he went to take the seat next to Jennifer. John moved to sit on the other side of the table. It was then Elizabeth noticed the baby Teyla was cradling in one arm. "Oh, Teyla," she said as she looked at the baby.

Teyla stepped closer to her, gently raising the baby and motioning for Elizabeth to take him. She did so, carefully holding it in both of her arms. "Hey there," she said, gently rocking it. "You're such a big boy," she cooed. With a little reluctance she handed him back to Teyla, and took a seat next to John while Teyla took the seat next to her. Almost in unison they all began to pass around the food which consisted mainly of pork and coleslaw.

"This is good," Ronon said as he chewed on some pork, his usual lack of emotion making Elizabeth wonder if he was being sarcastic.

Rodney was the next to take a few bites of the food, as he put a piece of the pork in his mouth he had his eyes tightly shut. Then he opened them in surprise and swallowed. "Wow, it really is good..." Rodney let out an umph of air, leading Elizabeth to believe Jennifer had just hit him in the ribs, "what I mean to say is you've really... really, really outdone yourself this time. You should cook barbecue all the time!"

Teyla smiled, clearly pleased. John dug into the coleslaw and nodded, "Yep, just like KFC." Though she didn't understand this statement, Teyla's smile widened.

Jennifer seemed just as surprised as Rodney had been when she tasted the food, but to her credit she managed to only sound slightly surprised, "Wow, this is great."

Elizabeth chewed a piece of the meat, and nodded in agreement as she swallowed, "I wouldn't have expected anything less."

Teyla was beaming at the table now, clearly very proud of her work, "Thank you."

They ate in silence for a while, then Rodney said, "Oh, hey, we're going back to Pegasus." The others looked up in surprise at this. 'What' and 'hows' were exclaimed from Jennifer, Teyla and Ronon at the same time.

"We're getting a ZPM and heading out," John explained.

"I have to admit," Jennifer said, "I was starting to miss Pegasus a little."

Teyla nodded, "I would have gladly stayed here... but I am a little relieved we will be returning."

"It sucks having to sign out to leave the city," Ronon said. "I'm glad we're leaving."

"Yeah, well," John started, "getting attacked by a killer bug tends to make you attached to a place."

"Or almost dying from starvation because of a force shield," Rodney supplied.

"Getting trapped on a hive ship," Ronon added.

"Taken hostage on a planet," Jennifer said.

"Being kidnapped," Teyla said.

Elizabeth had a crooked grin as she spoke up, "or dying."

There was a slight silence before the others started to laugh. "Having a stupid clone show up!" Rodney added. They kept adding things to the list all night, until finally Jennifer went into doctor-mode and insisted everyone get sleep. Jennifer and Rodney not-so-subtly headed out together. Ronon and Teyla headed on way to their rooms while John and Elizabeth headed the opposite way to their rooms.

They walked in silence, reaching her room first. She swiped her hand over the sensor and was about to walk through the door when she was surprised to hear John speak, "Hey."

She turned, now half in her room and half out of it. He pursed his lips and shifted on his feet, looking uncomfortable as he usually did when he had anything of emotional meaning to say. She said nothing, allowing him the time he needed.

"You gonna talk to that goa'uld tomorrow?"

"It depends if Woolsey wants me to, if he gets back first he may want to handle it himself." John nodded to this, shifted on his feet for another moment before he raised his head and looked at her.

"Welcome back home, Elizabeth."

"John..." she paused. There were things she wanted to tell him, like 'thank you' or 'I know you kept my father's pocket watch wound' or 'I'm sorry I lied to you when I was a replicator' or 'you're my closest friend' instead she said, "I didn't see the vase you gave me in my things, what happened to it?"

He looked a little sheepish as he responded, "It's in my room. I'll bring it by later." He shifted uncomfortably again, and she was surprised when he continued, "I wanted to leave part of you unpacked." She stared at him, overwhelming warmth rising in her stomach at how touched the gesture made her feel. "G'night," he said, turning to leave.

"Good night," she nodded to him, moving back to change into pajamas and then collapse into her bed. iWelcome back home/i, the words rolled around in her head as her mouth subconsciously spread into a smile and she fell into a blissful sleep.


	4. Chapter 4

Elizabeth stood next to Mr. Woolsey as the jumper arrived. He'd insisted that she be there along with him since she'd been the one who had brokered the deal. On Woolsey's other side stood John, and behind him was a very eager Rodney. Teyla and Ronon were on either side of Rodney, the flag ship team of Atlantis was ready to greet the new team.

The jumper landed in the docking bay, and didn't move. Another moment passed before Rodney cleared his throat as they all waited for the new team to reveal themselves. They didn't. "Maybe the door is stuck," John suggested casually, but when Elizabeth turned to look at him she could tell every muscle in his body was tense. His team could also pick this up; Ronon had his hand on the gun at his side.

Finally the jumper's door opened. First all Elizabeth heard was a slight clattering, and looking down she saw a small green object rolling towards them. "Down!" John yelled and the next thing she knew there was a body dragging her to a corner of the bay and pinning her against the floor and a corner wall she felt hands over her ears. A flash erupted and Elizabeth partially lost her hearing and sight, grimacing at the feeling of being in complete limbo.

Her vision cleared mere seconds later, but the scene in front of her was very different. As she raised her head she saw men in Atlantis uniforms with Russian patches on their arms walking off the jumper and out of the docking bay. Elizabeth, disoriented, started to ask them for help but felt a hand clamp shut over her mouth. She turned to see John shaking his head and indicating for her to be quiet. She nodded and he removed his hand.

In an instant he was gone, slinking behind the jumper and leaving her on her own. When he returned she was alarmed to see Rodney, Ronon and John dragging a body, she moved herself to a crouching position as they got closer and she saw that it was Teyla who was being dragged. John nodded to her, and then motioned to the jumper that they'd just been ambushed from. With a few hand signals Rodney and Ronon raised their weapons and made sure the jumper was clear, Rodney came back and nodded to the others and they entered it. Elizabeth immediately noticed the two soldiers that had been sent to escort the team collapsed in the front of the jumper, fatal wounds on both. John checked their pulses with a frown, then closed the door and put up the shield. In the middle of the jumper was a large box, which Rodney immediately went to and opened, it contained the ZPM.

Elizabeth moved to Teyla, checking her pulse. "She'll be okay," John yelled, his hearing off from the bomb, "just got knocked out."

"Woolsey?" Rodney asked.

John shook his head, "Didn't see him. I think the Russians took him."

"Okay," Rodney yelled, "the ZPM appears to be fully functional, they must have let the soldiers check it. So what the hell do they want?"

"They aren't Russians," Elizabeth said, her voice lower because her ears had been covered.

"What?" John yelled. She shook her head, raising her voice.

"They aren't Russians! They would never risk this. My best bet is Athena arranged this whole thing."

Ronon nodded, "So we shoot them?"

Elizabeth looked to John for the answer to this since Woolsey was missing, but he shook his head. "I seem to remember you being put in charge of speaking for Atlantis."

"Not like this," she argued, "this isn't my place."

"What?" He yelled, "Did anyone catch that?"

"Nope," Ronon smiled slightly.

"She said-" Rodney began, but John glared at him, "oh, no... nope."

Elizabeth shook her head, lowering it for a moment before she took in a deep breath and spoke, "Colonel Sheppard, we must alert the city to this problem."

"Communications are down," he replied.

"Of course they are," she groaned, the situation feeling very familiar. "Very well. If they're trying to take the city we'll assume they'll go for the control room. We have to reclaim Atlantis as soon as possible."

John nodded, "Sounds good. Let's head out." At that moment Teyla shifted with a groan, and instantly the others surrounded her. She popped up as if waking from a nightmare.

"I could not protect Mr. Woolsey," she said, "where is he?"

John rested a hand on her shoulder. "We think they got him. We'll get him back, it isn't your fault, none of us saw this coming." Elizabeth grimaced at the statement. She should have been the one to see it coming, the negotiation had been too easy, too simple. She shoved the thoughts aside, now was not the time for them. "You okay?" John asked Teyla, she nodded as Ronon helped her to her feet.

"Right," John said, "Teyla and Rodney watch our six, Ronon you're with me in front. Elizabeth, stay between us."

Elizabeth nodded, wishing she could be of more use but fully trusting John's military judgment. They headed out, weapons raised and ready. What they found was not reassuring, the hallway just outside the jumper bay was burned badly, likely from a grenade.

They moved through hallway after hallway, finding many personnel badly injured and unconscious or worse. John and Ronon rounded a corner, and suddenly the very loud sound of guns erupting could be heard. They quickly moved out of range, then in a well practiced unison they leaned into range and both began to shoot. John's arm shot back at an unnatural speed, and he grimaced as he collapsed to a sitting position against the wall. Elizabeth lowered herself by him, "John?"

He let out a grunt of pain, and she saw blood spreading on his arm. "Just a little gunshot wound," he muttered as she quickly applied pressure to it without thinking. Ronon shot a few more blasts before he moved next to John.

"I got one. I think they're wearing armor under the clothes."

"Woolsey?" Elizabeth asked, her hand not moving from John's shoulder.

Ronon nodded, "They had him. Unconscious and on the floor."

Elizabeth frowned, "They know he's the leader... they want to use him as a bargaining chip for our surrender, no doubt."

"How cliche," John grunted as he pushed himself to his feet.

"Colonel John Sheppard," a voice rang out. "We have your leader. You and your team will surrender now."

"See? Cliche," John muttered, and then he turned to Elizabeth, a light bulb practically lighting above his head.

"Yeah, well see," he yelled back, "my team isn't here."

"We know Ronon Dex is with you, as well as Teyla Emmagan and Rodney McKay. You will show yourselves," the voice responded.

John grinned, "Gotta love evil monologues." He nodded to Elizabeth, his voice a low whisper, "They don't know who you are, or that you're here. Must not have seen you when the bomb went off. Okay, now listen," he ripped a flash bomb off his vest, similar to the one they'd experienced before, "pull off the top, wait five seconds, then chug it as hard as you can at the bad guys. Got it?" He didn't wait for a response, instead he motioned towards the rest of the team.

"John," Elizabeth hissed, but he was already stepping out into the hall with his hands raised. Ronon followed his lead and Teyla and Rodney were right behind him.

"Right, you got us," John said, "very clever... steal the leader, catch the team, run the city. You guys work for Athena, huh?"

"She is our goddess," one of the men responded.

"Oh come on," Rodney said, "the Jaffa are free now!"

"We are not Jaffa, they were not loyal, we simply see the light," the man replied. Elizabeth took in a deep breath, pulling off the top of the grenade and then after counting to five, throwing the grenade down the hallway as far as she could. She covered her own ears this time, quickly moving back to kneel behind the wall. She heard the muffled sound of orders yelled by the other men, and then absolute silence as a white flash flared out from the hall. Elizabeth raised her head, but was surprised to see John looking straight at her.

"Run!" He screamed. Without another thought she rushed down the hallway. She turned to see a white flash. Her vision was temporarily gone again, but she took steps forward as it began to come back.

On the floor she saw Ronon, Rodney, Teyla and John unconscious. Unnerved she reached down and picked up John's gun, holding it close to her. She looked down the hall to see a single one of Athena's men rounding the corner back towards her, the others were unconscious. Her head was ringing and she was fully aware this had not been the plan. The man held the still unconscious Woolsey and was using him as a body shield. "I want immunity," he shouted across the hall.

"Okay," Elizabeth yelled back, not at all surprised by how quickly the man's loyalty had died, "we'll give you full immunity."

The man growled, "You're lying."

"No," Elizabeth said, "I was stalling. Men, take him into custody." He turned quickly, surprised to see a completely empty hall where he'd expected the guards she was talking to. In this brief moment she raised John's gun and shot the man, who quickly fell to the ground. She let out a sigh, running down the hall to check on Woolsey, who appeared to be uninjured but unconscious.

Later the men remaining were bound and the rest of Atlantis was alerted to the failed coup. Teyla, Rodney and Ronon quickly recovered, while John and Woolsey were taken to the med area. Elizabeth helped out in binding the men until she was practically dragged away to be examined. When Dr. Keller informed her she was fine but should rest she immediately went back to work.

After contacting Russia and finding out that the men who contacted them had, in fact, been impostors and the transmissions they had heard had been false, Elizabeth contacted the SGC and alerted them to the situation. Athena's men were sent to the SGC for holding and questioning while Rodney quickly set up the ZPM.

She made her way to the infirmary, checking on Woolsey who remained unconscious but in good health and finding John sitting on a seat in the corner of the room, his legs propped up as he played a gameboy with one arm in a sling.

She sat across from him, "How's the arm?"

"Fine. Better than the men we lost," he said, not looking at her. She nodded and they both remained silent for a moment.

"I should have known," she said quietly, thinking about the negotiation again.

"You weren't the one in charge," John replied, his eyes not leaving his gameboy. "When you were in charge you saved the city." She didn't respond to this, knowing full and well that the conversation could be a never ending one where she insisted it was her fault and he insisted it was his.

"Colonel Sheppard? Dr. Weir?" Woolsey croaked, and the two of them turned to him, moving to either side of his bed. "What happened?"

"Athena's people tried to raid the city," John replied. Woolsey closed his eyes and nodded. "Casualty rate?"

"Low," John said, "but we lost some people."

Woolsey let out a low, almost inaudible sigh at this.

"Dr. Weir?" A voice came over her com device.

"Yes?" She asked in confusion.

"A Dr. Jackson is here."

"Oh god," she said, "I completely forgot... he's going to be staying with us for a few months to study some artifacts here. I'll be right there."

She ran off, leaving John and Woolsey alone. "She's an extraordinary woman," Woolsey said quietly.

"She's Dr. Elizabeth Weir," John replied.

She met Daniel in the docking bay, and found him lugging a few suitcases. She was surprised to see Vala jump out from behind him, carrying a handful of books. "Vala?"

"I'm his assistant," she beamed. He let out a low sigh.

"Daniel, I'm sorry, we've been a little... busy." He looked beyond her to the hall with burnt walls and nodded.

"Yeah, I see that. Let me guess, I can't stay?" Daniel asked.

"He always whines about how he can't come to Atlantis because of this or that, usually blames me," Vala said.

"You held me prisoner aboard The Prometheus and tied a goa'uld bracelet- you know what, nevermind," he muttered.

Elizabeth raised an eyebrow but shook her head, "This incident has only made us more determined to leave. We'll be heading out at the scheduled time, we're glad to have you aboard."

"Thanks for inviting me," he said, "with no major threats to mankind I actually have a chance to just study the artifacts here until I return to SG1."

She nodded, smiling at both of them as she told a nearby guard to escort them to empty rooms and then to the lab Daniel would be occupying for his stay. As they left she heard Daniel say, "If you're going to assist me shouldn't you actually be carrying something?"

"Oh, I thought I'd be more like a Vanna White assistant," Vala replied. Elizabeth shook her head in amusement at the two, letting out a small sigh as the tension of the day was broken.

It was with great relief an hour later that the city took off. Elizabeth, with nothing left to do, walked the city taking in the familiar sites of it all. Eventually she made her way back to her room and began to set up a few decorations from her boxes.

Her door opened and she turned to see Rodney. "Hey, wanna get some dinner? Teyla was a little busy, what with the... being attacked and all so we're going to the mess hall."

"Sure," she said as she finished arranging a few items before she followed Rodney out of the room. She was surprised when they ended up in the gateroom. It was filled with people who were lining both sides of the room. She paused in surprise, "Rodney... what..." she began, but was surprised to turn and see Rodney had left her and was making a light jog up the stairs.

Her eyes followed him, and she froze. At the top of the stairs stood Richard Woolsey, at his side John Sheppard. Behind them stood Teyla, Ronon and Rodney. She saw Daniel and Vala were at the top of the stairs, to the side. Vala was grinning, and poked Daniel when she saw Elizabeth. All the eyes in the room were on her.

"In light of recent events," Woolsey began, his voice echoing across the room, "it has been decided that there is a promotion in order. Dr. Elizabeth Weir, please step forward."

She was shocked, and just stood where she was for a few moments before finally stepping up the stairs, all eyes in the room following her. When she reached the top she stood beside John, he nodded to her with a large grin on his face. She smiled back, still utterly surprised.

"Elizabeth Weir," Woolsey continued as she turned to face him, "you have shown incredible dedication to this city. You gave your own life in the service of the greater good, and not a single person here doubts that you would do it again. You were the first person to lead this mission, you set the foundation of courage and determination that we still follow today." A blush spread across her face at the words, she looked to John, Teyla, Ronon, and Rodney and they were all smiling back at her.

"As such, it is my very great honor," Woolsey said, "to announce you as the new senior member of this mission."

Her jaw dropped, her mouth moved as if to say words but she could find none. Finally she turned to Woolsey, her eyes glistening, "What will you do?"

"Oh, I'll be here," he said, "I didn't say you're the only senior member of the mission. Anyway, someone needs to deal with the IOA, and I've gotten pretty good at stalling the wraith. It's a big city, Dr. Weir, I'm sure I can find something to do." She smiled widely at him. "On a completely unrelated note," he added, "I've decided I don't quite like my office. It's too... big. You'll just have to do with it while I move to my preferred office, just next to the conference room."

She leaned in and hugged him very briefly with complete excitement, and then pulled away, "Thank you."

"It was never a choice," he replied quietly. "You made that clear today." She tucked a strand of her hair behind her ear, her cheeks a rosy red as she took in the overwhelming situation. Everyone in the room began to clap, and this only made the color in her cheeks deepen.

"You know," John said as he leaned in closer to her, "this is generally the time for a speech."

She bit her lip and turned towards the room, as the applause died down she spoke. "Atlantis... is more than a mission," she began. "It's a home... those of you who have been here long enough know that to be true. The times here can get pretty rough, and they do, but the city will always remain. This will always be home." She shook her head, now completely choked up. The room burst into applause again.

After that it was right back to work as the city landed back onto the planet it'd been on before. Elizabeth went back to overseeing the everyday activities of Atlantis. That night she found herself leaned over on the balcony, the wind flowing through her now much longer hair.

"Couldn't sleep?" John leaned his back on the rail beside her. She smiled at him.

"Back to work, back to not sleeping," she replied.

"Set up the office yet?"

"Ironically I haven't had the chance," she smirked, "work is preventing me from setting up a base to work out of." She stood and turned so that she was facing the same way he was. "How's the arm?"

"The doc says it'll heal up pretty fast," he replied, "I've got to remember to stop getting shot."

"And your team?"

"Good. Ronon's a little sore he got knocked out and you saved our asses... Teyla's still holding the guilt over not saving Woolsey in the first place, and Rodney is probably somewhere still playing with the ZPM."

"And you?" She asked, lightly turning to face him. His eyes raised to meet hers. The gaze lasted for a few moments before he grinned and broke eye contact.

"Didn't I just tell you I got shot?"

"Right," she replied in amusement. Then she turned back to look over the city, "You know, it seems absurd... all of this. If I had caught the plan in the first place-"

"We wouldn't have a ZPM," John cut her off.

"A ZPM they no doubt intended to use in the most destructive way possible," Elizabeth replied.

"But that we got," John said. "If this had played out any differently we'd be back in San Francisco arguing with every so-called diplomat or negotiator on the planet." Elizabeth raised her eyebrows at him curiously. "Not that there's anything wrong with diplomats," he added with a slight smirk. Then he was serious again, "This is how it had to play out."

She shook her head, and opened her mouth but he firmly repeated, "This is how it had to play out."

"You were shot, John."

"And I'd get shot again if this is the end to that," he replied with a shrug.

"John, I-" She paused, considering the possible ends to the sentence.

I'm sorry I lied.

I'm sorry you were the one who had to leave me with the replicators.

I never stopped thinking about you.

I know you're the one who fought to bring me back.

I have no doubt I watched over you when I was ascended.

I missed you.

He took in a deep breath as he turned to face her. Their eyes met, raw emotion sparkling from both of them. He considered her for a moment before considering the possible replies to her unspoken sentence.

It kills me that I couldn't save you.

I should never have left you with the replicators.

I've never been happier to see a person in my life.

I kept the damn watch wound because it reminded me of how much time had passed.

I always felt like you were with me.

I missed you.

"I know," he replied, and she knew that he did. "So, I heard you were found naked in the woods." She raised an eyebrow at him and he tried to look completely innocent but failed as he began to grin.

That was when Rodney came flying out onto the balcony flailing his arms.

"You guys are not going to believe this, we just found a room with robots!" Elizabeth and John both just stared at him, "...okay, you might believe that. But the robots look like Wraith and might teach us things we don't know about them."

This got their attention, "Are they safe?" Elizabeth asked.

Rodney rolled his eyes at her, "No, we're about to have a robot attack." John raised an eyebrow at him, "We're... not," Rodney insisted, "they're safe. Come on!" He ran back inside, and after a shared shrug Elizabeth and John followed him.

It was just another day on the job.

**A/N:** So that's it, though I am writing an epilogue for this and if that feels right I'll post it too. Possibly a little bit too mushy and fluffy, but what can I say? I'm a shipper and I love Elizabeth. Lord knows she deserved a happy ending, and I was compelled to write one for her. :)


End file.
